Methods for analysing genetic material often require amplification of the nucleic acid sample as an initial step. This sometimes require the step of separating the two strands of a double-stranded DNA sample (dsDNA). In doing so, a related art method known as the Polymerase Chain Reaction (PCR) is employed. According to one variant of this method the dsDNA sample is amplified by the supply of a primer pair of which one is biotinylated, to a receptacle, which holds the solution containing the dsDNA sample. Streptavidin coated beads are then added to the solution, and by also adding a binding buffer the amplified dsDNA will be immobilised on the beads.
These beads may be made of sepharose, and one related art method for preparing single stranded DNA (ssDNA) is as follows: First, the receptacle holding the immobilised dsDNA is put on a vacuum station. The bottom of the receptacle is provided with a filter, which pore diameter is less than the size of the sepharose beads. Thus, when an under-pressure is applied on the underside of the filter the beads in the solution will be left on the filter, while the solution is drained away through the filter to, e.g. a liquid collector. In a next step, sodium hydroxide is supplied to the receptacle, which will separate the strands of the dsDNA into ssDNA, whereupon the sodium hydroxide is drained away. Thus, the ssDNA strands which are not bound to the beads are also drained away, while the bound ssDNA strands remain caught on the filter. In yet a further step, remaining sodium hydroxide is neutralised by means of an addition of washing buffer one or several times, and in a final step, in which the under-pressure is removed, a solution for re-suspending the caught beads in the solution is added. These beads having attached ssDNA strands are now ready to be transferred from this receptacle to an other receptacle for further preparation, or for analysis of the ssDNA.
However, it is difficult to fully re-suspend all beads in the solution since the beads are caught in the filter, and easily stick there despite the re-suspension attempts. Thus, trying to catch all beads by means of pipetting is difficult. Moreover, the situation is made worse when the heights of the liquid columns of the wells are low which yet render difficulties to the pipetting. Furthermore, the receptacle is commonly in the form of a multi-well receptacle, such as a Micro Titre Plate (MTP), having e.g. 96, 384, 1536 or 6144 separate wells, whereby a repetitive pipetting is disadvantageous from a strain injury point of view.
An other related art method disclosed in GB 99 233 249 uses magnetic beads instead of sepharose beads. According to this method a magnet is introduced into the receptacle, e.g. a well of a MTP, whereby the streptavidin coated magnetic beads are attracted to and hold by the magnet. Thus, the magnetic beads as well as the bound dsDNA may be removed from this receptacle and transferred to an other receptacle, in which e.g. a strand separating solution, such as sodium hydroxide is contained. Accordingly, the dsDNA will be separated into ssDNA, whereby the first strands are suspended in the solution, and optionally drained away, while the second strands remain bound to the beads. These latter strands may now be transferred to an other receptacle for further preparation, or for analysis.
However, magnetic beads are more expensive than sepharose beads, and the use of sepharose beads also results in better quality in a sequencing-by-synthesis method.
Furthermore, another related art method disclosed in U.S. Pat. No. 6,156,550 is related to transferring beads from one solution to another solution. This method describes how sepharose beads can be attached to a surface of a polymer. The drawback with beads bound to a support is that beads bound to a surface do not behave biochemically or physically similar to beads in a solution, thus further analysis of the ssDNA will be difficult.
In an other related art method disclosed in JP 58223759 beads are moved between two test tubes. A nozzle 16 is immersed in a first test tube 17 where it attracts a bead B by means of a vacuum. Then, the nozzle 16 is moved to a second test tube 18 where a back pressure is applied so as to release the bead B in the second test tube. During the whole movement the vacuum prevails within the nozzle. However, the nozzle is only capable of moving large beads, which are attracted to and stuck on the tip of the nozzle. In case of small beads, such beads would be drained away together with the liquid contained in the test tubes.